RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029652
(190 letters)
>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} SCOP: c.56.3.1 PDB:
1rym_A 1ryn_A
Length = 205
Score = 253 bits (649), Expect = 4e-87
Identities = 96/157 (61%), Positives = 121/157 (77%)
Query: 18 PWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAK 77
PWL GLGNPG+KY GTRHNVGFEM+D A +GI+MNT+ K+ G G +G+ PVL+ K
Sbjct: 17 PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVK 76
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
PQ+YMN SGE+ GPLAAYY++PL +L+ +DD LP GVLRL+ GGHG HNGL++V+ +
Sbjct: 77 PQSYMNYSGEAIGPLAAYYQVPLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIEH 136
Query: 138 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
G REF RL IGIG PPG+MDP+AFLLQKF++ R
Sbjct: 137 LDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERV 173
>2z2i_A PTH, peptidyl-tRNA hydrolase; protein synthesis; 1.98A
{Mycobacterium tuberculosis} PDB: 2z2j_A 2z2k_A 3tck_A
3tcn_A 3td2_A 3td6_A 2jrc_A 3p2j_A 3kk0_A 3kjz_A
Length = 191
Score = 239 bits (612), Expect = 1e-81
Identities = 73/160 (45%), Positives = 93/160 (58%), Gaps = 2/160 (1%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTV-HCKATFGQGFVGDAPVL 74
A P L VGLGNPG Y TRHN+GF + D A G A G ++
Sbjct: 2 AEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLV 61
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSV 134
LAKP+ YMN SG GPLA +Y + ++V HDD+ L G +RL+ GG GGHNGL+SV
Sbjct: 62 LAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSV 121
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
+ G ++F R+RIGIGRPPG+ DP AF+L+ F R
Sbjct: 122 VAAL-GTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERA 160
>4fno_A PTH, peptidyl-tRNA hydrolase; 2.25A {Pseudomonas aeruginosa} PDB:
4djj_A* 4erx_A 4dhw_A
Length = 194
Score = 233 bits (597), Expect = 3e-79
Identities = 58/160 (36%), Positives = 85/160 (53%), Gaps = 1/160 (0%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVL 74
L VGLGNPG +Y TRHN G ++ A +QG+S+ G+ V
Sbjct: 2 TAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVR 61
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSV 134
L P TYMN SG+S LA ++++ + +LV HD++ +P GV +L+ GGHGGHNGL+ +
Sbjct: 62 LLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDI 121
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
+ F RLR+GIG P ++L + +E
Sbjct: 122 IAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQE 161
>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli} SCOP: c.56.3.1
PDB: 3ofv_A
Length = 193
Score = 226 bits (579), Expect = 1e-76
Identities = 58/157 (36%), Positives = 85/157 (54%), Gaps = 1/157 (0%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGL NPG +Y TRHN G +D AE + + +G V L
Sbjct: 3 KLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLV 62
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
P T+MNLSG++ +A+++++ + +LV HD++ LP GV + + GGHGGHNGLK +++
Sbjct: 63 PTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISK 122
Query: 138 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARE 174
N F RLRIGIG P + F+L K ++
Sbjct: 123 LGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQK 159
>3nea_A PTH, peptidyl-tRNA hydrolase; 2.25A {Francisella tularensis subsp}
Length = 207
Score = 222 bits (568), Expect = 9e-75
Identities = 54/156 (34%), Positives = 84/156 (53%), Gaps = 2/156 (1%)
Query: 16 ARPWLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVL 74
+ + +GLGN G +Y+ TRHNVG I A+ S ++ + + V+
Sbjct: 21 PKIKMIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVV 80
Query: 75 LAKPQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSV 134
L P TYMN SG + +A +YK+ +LV HD++ + G +RL+ GGHGGHNGL+S+
Sbjct: 81 LVFPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRSI 140
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNA 170
+ G ++ RLRIGIG P + ++L +
Sbjct: 141 NQHL-GTNDYLRLRIGIGHPGHKSKVANYVLSNPSI 175
>3v2i_A PTH, peptidyl-tRNA hydrolase; ssgcid, seattle structural genomics
center for infectious DI RNA; HET: CIT; 1.65A
{Burkholderia thailandensis E264}
Length = 222
Score = 216 bits (552), Expect = 4e-72
Identities = 61/163 (37%), Positives = 89/163 (54%), Gaps = 12/163 (7%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGLGNPG +Y TRHN GF ++D A G ++ + + + V L +
Sbjct: 24 KLIVGLGNPGAEYTATRHNAGFWLVDQLAREAGATLRDERRFHGFYAKARLYGEEVHLLE 83
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
PQTYMN SG+S LA ++K+ N +LV HD++ LP G ++L+ GG GGHNGLK + +
Sbjct: 84 PQTYMNRSGQSVVALAHFFKILPNEILVAHDELDLPPGAVKLKLGGGSGGHNGLKDISAH 143
Query: 138 FRGNREFARLRIGIGRPP----------GQMDPKAFLLQKFNA 170
++++ RLRIGIG P + D F+L+
Sbjct: 144 L-SSQQYWRLRIGIGHPRDMIPESARAGAKPDVANFVLKPPRK 185
>4fop_A PTH, peptidyl-tRNA hydrolase; 1.86A {Acinetobacter baumannii}
Length = 193
Score = 215 bits (549), Expect = 5e-72
Identities = 59/153 (38%), Positives = 86/153 (56%), Gaps = 3/153 (1%)
Query: 19 WLFVGLGNPGDKYKGTRHNVGFEMIDAFAESQGISMNTVH-CKATFGQGFVGDAPVLLAK 77
L VGLGNPG +Y TRHN GF ++ A+ GI++ G+G + V L
Sbjct: 5 SLIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLL 64
Query: 78 PQTYMNLSGESTGPLAAYYKLPLNRVLVFHDDMGLPCGVLRLRHNGGHGGHNGLKSVMNN 137
P TYMN SG+S P + +Y++ +L+ HD++ + GV+RL+ GGHGGHNGL+ ++ +
Sbjct: 65 PMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVPH 124
Query: 138 FRGNREFARLRIGIGRPPGQMDPKAFLLQKFNA 170
F RLRIGIG P + +L K +
Sbjct: 125 I--GPNFHRLRIGIGHPGSKERVSGHVLGKAPS 155
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 37.7 bits (87), Expect = 0.002
Identities = 45/244 (18%), Positives = 73/244 (29%), Gaps = 88/244 (36%)
Query: 20 LFVGLGNPGD-------KYKGTRHNVGFEMIDAFAES-QGISMNTVHCKATFGQGFVGDA 71
+F G GN D Y+ VG ++I AE+ + T+ + F QG +
Sbjct: 159 IFGGQGNTDDYFEELRDLYQTYHVLVG-DLIKFSAETLSELIRTTLDAEKVFTQGL--NI 215
Query: 72 PVLLAKPQT-----YMNLSGESTGPL-----AAYYKLPLNRVLVFHDDMGLPCGVLRLRH 121
L P Y+ LS + PL A+Y +V +G G LR
Sbjct: 216 LEWLENPSNTPDKDYL-LSIPISCPLIGVIQLAHY-------VVTAKLLGFTPGELRSYL 267
Query: 122 NG--GHGG------------------HNGLKSVMNNF----RGNREFARLRI-------- 149
G GH + K++ F R + +
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDS 327
Query: 150 ---GIGRP-PGQM-----DPKAFL---LQKFNA-IARERDISF------DCIIV------ 184
G P P M + + + K N+ + + + ++V
Sbjct: 328 LENNEGVPSP--MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQS 385
Query: 185 FYGL 188
YGL
Sbjct: 386 LYGL 389
>2pd1_A Hypothetical protein; unknown function, NE2512 protein, structural
genomics, APC72 2, protein structure initiative; 1.86A
{Nitrosomonas europaea} SCOP: d.58.4.11
Length = 104
Score = 29.1 bits (65), Expect = 0.38
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 10/60 (16%)
Query: 40 FEMIDAFAESQGISMNTVHCKATFGQGFVGDAPVLLAKPQTYMNLSGESTGPLAAYYKLP 99
F + DAFA+ G H + +A LL+ P + LAA KLP
Sbjct: 52 FGVFDAFADEAGRQ---AHLNGQIAAALMANAATLLSSPPNIEKVE-----LLAA--KLP 101
>3a8r_A Putative uncharacterized protein; EF-hand, membrane,
oxidoreductase, transmembrane, calcium BI protein; 2.40A
{Oryza sativa japonica group}
Length = 179
Score = 27.3 bits (60), Expect = 2.8
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 127 GHNGLKSVMNNFRGNREFARL-RIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCI 182
G++G +V F + L R G+ G F +Q F+++AR+R I +
Sbjct: 23 GNDGWAAVEKRFNQLQVDGVLLRSRFGKCIGMDGSDEFAVQMFDSLARKRGIVKQVL 79
>3dmp_A Uracil phosphoribosyltransferase; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid; 2.60A {Burkholderia pseudomallei}
Length = 217
Score = 26.8 bits (59), Expect = 4.5
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 23 GLGNPGDKYKGTRH 36
GLG+ GD+ GT++
Sbjct: 204 GLGDAGDRLFGTKN 217
>3kff_A MUP 4, major urinary protein 4; pheromone, lipocalin, beta barrel,
DI bond, pheromone-binding, secreted, transport,
transport Pro; 0.96A {Mus musculus} PDB: 3kfg_A 3kfh_A
3kfi_A 2l9c_A 2lb6_A 1i06_A 1i05_A* 1i04_A 1mup_A 1znd_A
1qy0_A* 1qy2_A* 1qy1_A 1zne_A 1zng_A 1znh_A 1znk_A*
1znl_A* 2dm5_A* 2ozq_A ...
Length = 162
Score = 26.5 bits (58), Expect = 4.8
Identities = 10/51 (19%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCIIVF 185
+ N + + F + + GR ++ +KF + E I + II
Sbjct: 105 LINEKDGKTFQLMEL-YGRKA-DLNSDI--KEKFVKLCEEHGIIKENIIDL 151
>1gm6_A SAL, salivary lipocalin; odorant-binding protein; HET: NAG; 2.13A
{Sus scrofa} SCOP: b.60.1.1
Length = 175
Score = 26.1 bits (57), Expect = 5.5
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCIIVF 185
+ + G++ F + GR P ++PK KF I ++ I + II
Sbjct: 108 LVDVNGDKTFQLMEF-YGRKP-DVEPKL--KDKFVEICQQYGIIKENIIDL 154
>1e5p_A Aphrodisin; lipocalin, pheromone, hamster,; HET: MSE; 1.63A
{Mesocricetus auratus} SCOP: b.60.1.1
Length = 151
Score = 26.1 bits (57), Expect = 5.9
Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCIIVF 185
N R +E + + G+ + P+ + A E+ I + I+
Sbjct: 97 KNMDRAGQETNMIVV-AGKGN-ALTPEE--NEILVQFAHEKKIPVENILNI 143
>2ra6_A Trichosurin; lipocalin, beta barrel, glycoprotein, MILK protein,
secreted, transport, transport protein; 1.50A
{Trichosurus vulpecula} PDB: 2r73_A 2r74_A
Length = 166
Score = 26.2 bits (57), Expect = 6.5
Identities = 7/51 (13%), Positives = 16/51 (31%), Gaps = 4/51 (7%)
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCIIVF 185
N+ + + GR P + + ++F R + I+
Sbjct: 114 FYNYHDGKVNVVANL-FGRTP-NLSNEI--KKRFEEDFMNRGFRRENILDI 160
>2a2u_A Protein (alpha-2U-globulin); lipid binding protein; 2.50A {Rattus
norvegicus} SCOP: b.60.1.1 PDB: 2a2g_A
Length = 181
Score = 25.8 bits (56), Expect = 8.6
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCIIVF 185
+ NF+ F + + GR + +KF + I+ D II
Sbjct: 124 LINFKNGETFQLMVL-YGRTK-DLSSDI--KEKFAKLCEAHGITRDNIIDL 170
>1dzk_A PIG OBP, odorant-binding protein; lipocalin, transport, olfaction,
sensory transduction; HET: PRZ; 1.48A {Sus scrofa} SCOP:
b.60.1.1 PDB: 1dzj_A* 1dzm_A* 1dzp_A* 1e00_A* 1e02_A*
1e06_A* 1hqp_A* 1a3y_A
Length = 157
Score = 25.7 bits (56), Expect = 8.7
Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCIIVF 185
+N + + +G+ ++ + L+KF + RE I + I+
Sbjct: 103 INVDEEGDKTIMTGL-LGKGT-DIEDQD--LEKFKEVTRENGIPEENIVNI 149
>3sao_A Extracellular fatty acid-binding protein; beta-barrel, siderophore
binding protein, transport protein; HET: NKN DBH; 1.80A
{Gallus gallus} PDB: 1jzu_A 2kt4_B* 2lbv_A*
Length = 160
Score = 25.7 bits (56), Expect = 8.9
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 135 MNNFRGNREFARLRIGIGRPPGQMDPKAFLLQKFNAIARERDISFDCIIVF 185
+ R +R+ R ++ P A + F +ARER+ + + + V
Sbjct: 99 ATRVKDGRTLHMMRL-YSRSR-EVSPTA--MAIFRKLARERNYTDEMVAVL 145
>1hh2_P NUSA, N utilization substance protein A; transcription regulation,
termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5
d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A
Length = 344
Score = 25.9 bits (58), Expect = 9.6
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 164 LLQKFNAIARERDISFDCII 183
LL+ + + E+ IS + +I
Sbjct: 5 LLEALDQLEEEKGISKEEVI 24
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.326 0.145 0.457
Gapped
Lambda K H
0.267 0.0826 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,080,891
Number of extensions: 181511
Number of successful extensions: 406
Number of sequences better than 10.0: 1
Number of HSP's gapped: 396
Number of HSP's successfully gapped: 24
Length of query: 190
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,244,745
Effective search space: 432963990
Effective search space used: 432963990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.4 bits)